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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.2.0] - 2026-03-19

Added

  • Explainability Engine: Every prediction now includes a reasoning chain and evidence aggregation.
  • Multi-layer Evidence Pipeline:
    • PROSITE motif scanning (built-in 1,800+ patterns).
    • EBI HMMER/InterPro web API integration.
    • UniProt REST API lookup for reviewed entries.
  • Novel Gene Discovery: New module to rank "Dark Matter" genes (no evidence) for research priority.
  • CLI Overhaul: New giae interpret, giae parse, and giae db commands.
  • Parallel Processing: Added --workers flag for multi-threaded genome interpretation.
  • Plugin System: Support for local BLAST+ and HMMER plugins.
  • Rich Reporting: Markdown and JSON output formats with stylized terminal tables.

Improved

  • Genome parsing logic for large GenBank and FASTA files.
  • Confidence scoring calibration based on evidence convergence.

Changed

  • Moved source code to src/ layout for better packaging compatibility.
  • Switched to hatchling as the build backend.

[0.1.0] - 2026-02-15

  • Initial internal release.
  • Basic motif scanning and GenBank parsing.